seq2fa.pl

#!/usr/bin/perl

use strict;
use warnings;

use Bio::PrimarySeq;
use Bio::SeqIO;
use Bio::Seq;

use IO::File;


my $seq = 'GGAAACAGCTATGACCATGATTACGCCAAGCTCAGAATTAACCCTCACTAAAGGGACTAGTCCTGCAGGTTTAAACGAATTCGCCCTTAATTCGCCCTTTGAAAAGATAATACATGCCAGGTAGCTCTGGTGCACTCCTT
TAATCCCAGCACTCAGGAGGCAGAAACAAGTGGATCTCTGTGAATTCGGGGTCAGCCTGGGCTACAGAGA
GTTTAAGTGTTGCCTGAGGAGTAACGCCTAAAATAGATCTTTGACCTCCACTTACACACGCACACACCAA
TAAATTAATAATAATTTTAAAAAGTGTAATACCCCTGTATTGAAAGAAAAAAAAAATCCCCTGGTCAACA
GAGTGAGTTCCGGGACAGCAGGGCTCTGTTACACAGAGAAACCCTGTCTCAGAAAAATAAACCAAGATGC
TACGGAGGCAGGCTGGAGCTGCTGCCATCTTCACGGCCCATGGTAAACGGGAGAGCTTGCTGGCCAGAAG
AACGTGAAGAAGCAGAGCGACTCAGCTCAGGGAAAGCACCGAGAAGATGGGCTTCTGCCCACAAGCAGAG
GACCAGGAGACCATGGAGCAGAAGCAGAAAACGGGCAGGAGGAACCCAAGTAGCTTCCGGCTTCCTGTCC
GACTCTCCTGCCCTGCACTGCCTGGAGCCAGGCCCACCGTGCTCCAGTTTCTTCCTGTAGTGCTCACAGG
TCCCTGCACTGATGGCATTCCCTTTGCCCCGAGTCTGTGGCGGGTTCCTTTTGTGCTTCCTTCCCTCCTG
TAGCCTCTCTCCCTCTGGGCCACTCCTGGGGTGGGGATGGGGGTGGCTACCCCTCCCCAGTGCTTTTTAT
TTCTGTAGGGCACACATCAAAGTATTAAAAGTAGCTTTGTATAAAAGACAAAACAAAACATAAACCATAA
AAACAATGAAAAAAATTGTAATTTTAATGGAAATCAGAGCAGCAGAGCCATGAAGAGCAAGACAGTTTGA
AGTGTTCCTCTGTGACCTCTGCTCCAGTTCCTGCCTTGAGGTTGCTGCCCTGAGCTCCTGCCCTGACTTC
CCTCTGTGATGTGTGACCTGGGAGTTGTAAGATGAAGTCAACCTTTTCTTCTCTGATTCCGTTTTGGTCA
TGGAGTTTTATCACGGCAGTATAAATCCAATCAAAGCAACGTGAATTGAATCGCCAGTTAGGAAAGTGCA
GCCTTAGGGAAGGGGGCGTCTTCTCTCAAGCAGTGATCTTCAGCAAACAGAACGGCCCCGTTGTCCTGTC
CCCATGGTGTCCCTTTCCCTTACCCCTCTTTGCCTAGCCATCTAAGCCCCTGCCTTTAGTGTACTTGTGG
ATTTTAATCACCTGCCTAACTGCACTCTGGCTTTGAAAATCAATCTACCAGTTTCTAAGCCACACATCCT
GTGCCTATGTCTTCCTTTTCATCTCCTTTACCCACATCTAGTTCTGACCTTTGAATCTCTCCCTGGACAT
GGTTGTCACCCCCATGCCAGCAGGTACTCTTATACTCCCATTAGCCCTGCACATTGCTGCCAAGTTCACC
TTAGGGTACCTCTTTGGTGCTGTCCCTGCTGGTGAGCAGAGTCCAAACCAGCCACTTCATCCTCCTCCAG
ACACTGCTATGCCCTGCAATTGACTCGATTCATAACTGACTGGGTGGACATGCAGGGGCTGGAGGAGGGT
GCTGGCAGATCTTCCCGTCTAGCTGCAAGGCAGGGCGCTACCTCCGTAAAGATGCAAGCGCAGCCCGCAC
AGGGGCCTGGGTTCCACAGTCCTGGCCATAGTCAGCTGGCATTCACAGAACAAAGCAGCCACTCTCTTCC
TCCCAGCCTCCTTTCCTGAGGAGAGAGGCCCTGCAATCACCTTCCCTCCATAACTACTTACAAGTCAACA
GCACTTCTCAGTGATATGGAACCATCGGGAATGGCTGTAAGTCACTGCCTCATCTGCCTCATCTTCTTAT
GGTTTCAGATATGAGCTAATGAAATGGCAGATGACAGGAGACAGAAATGTCACCTGCTTTAGTGGGGATG
CTGAACACTCATTGAGACTGGGCATCAGTTTTGCCGGATGGGAAACTGAGGCTCTCCTACTGTGACCTGC
GGGGAGGAGTGGCTCTCTCCTTGTCCCCAACTCCATACCCTAAGAAGTCAGATCACTAGACTCAGCATCC
CACCTGTAACCAATTCCATTGTCTTTTTTTCCTCCAGGCTTTGAACCAGTATGGCTGACCCTCGCCAGGA
GTTTGACACAATGGAAGACCATGCTGGAGATTACACTCTGCTCCAAGACCAAGAAGGAGACATGGACCAT
GGGGCCCAAACAGCGACTCTAGACTTAATTAACATGAGTAGATCTTCTAAGAACGTCATCAAGGAATTCA
TGAGATTCAAGGTTAAAATGGAAGGTACTGTTAACGGCCACGAATTCGAAATCGAAGGTGAAGGTGAGGG
TAGACCATATGAAGGTCACAACACAGTCAAGTTGAAGGTTACTAAGGGTGGTCCACTGCCATTCGCTTGG
GACATCTTGTCTCCACAATTCCAATACGGTTCTAAGGTCTACGTCAAGCACCCAGCTGACATTCCAGACT
ACAAGAAGTTGTCCTTCCCAGAAGGTTTCAAGGGCGAAGGGCGAATTCGCGGCCGCTAAATTCAATTCGC
CCTATAGTGAGTCGTATTACAATTCACTGGCCGTCGTTTTAC';
$seq =~s/\W//g;

$seq = Bio::PrimarySeq->new(
			    '-seq' => $seq,
			    '-alphabet' => 'dna',
			    '-id' => 'Tau_Primer3_PCR4');

my $seq_out = Bio::SeqIO->new('-file' => ">seq.fa",
			      '-format' => 'fasta');

$seq_out->write_seq($seq);


my $infile  = new IO::File;
my $outfile = new IO::File;

if ($infile->open("< seq.fa")) {
  if($outfile->open(">seq.fa2")){
    while (<$infile>){
      print $outfile "$_\n";
    }
    $infile->close;
    $outfile->close;
  }
}